Antimicrobial compositions and methods of use thereof

ABSTRACT

Described herein is a novel class of inhibitors of bacterial cell division. Several lines of evidence suggest the compounds disclosed herein specifically target the division process and have antibacterial activity in vitro and in vivo. The inhibitors are useful for treating subject in need of treatment for bacterial infections as will as for inhibiting bacterial growth, such as growth on contaminated surfaces.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a divisional of U.S. application Ser. No. 13/546,667filed on Jul. 11, 2012, which claims priority to U.S. ProvisionalApplication No. 61/506,294 filed on Jul. 11, 2011, both of which areincorporated herein by reference in their entirety.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH & DEVELOPMENT

This invention was made with government support under 11-CRHF-0-6055awarded by the USDA/NIFA. The government has certain rights in theinvention.

FIELD OF THE DISCLOSURE

The present disclosure is related to novel inhibitors of bacterial celldivision, and methods of use of the inhibitors.

BACKGROUND

In the past two decades, significant progress has been made towardsunderstanding the mechanistic complexity of bacterial cell division.Once viewed as a simple binary fission, it is now known that celldivision in bacteria involves a tubulin homolog, FtsZ. FtsZ polymersinitiate cell division and recruit downstream machinery for subsequentremodeling of the cell wall. Since FtsZ and the associated machineryplays a central role in forming the septum, several mechanisms exist toregulate its polymerization in both space and time. Perturbing thefunction of the components of this machinery directly, or the regulatoryprocesses on cell division, has become an attractive route forantibiotic discovery and development.

U.S. Patent Publication 2010/0273837, for example, discloses substitutedthiadiazolylmethoxybenzamide or thiadiazolylmethoxypyridylamides withsome inhibitory activity against Staphylococcus aureus, a Gram-positivepathogen. A specific compound that has been tested is PC190723, acompound identified by systematic modification of 3-methoxybenzamide.PC190723 was shown to protect mice from a normally lethal dose of theMRSA strain of Staphylococcus aureus.

What is needed are additional inhibitors of cell division withantimicrobial activity, particularly inhibitors effective against avariety of microorganisms.

BRIEF SUMMARY

In one aspect, a pharmaceutical composition comprises a cell divisioninhibitor and a pharmaceutically acceptable excipient, wherein the celldivision inhibitor is of Formula I or a pharmaceutically acceptable saltthereof:

G-Q-Y-Z-Ar   (I)

wherein

G is

wherein each instance of A is independently CH or N provided that thetotal number of N is 0 or 1;

R¹ is hydrogen, hydroxy, amino, halogen, cyano, C₁-C₆alkyl, C₁-C₆alkoxy,C₁-C₆haloalkyl, C₁-C₆haloalkoxy, aryl, or (aryl)alkyl;

X¹ is N, CR², O, or S;

X² is O, S, or NR⁴;

R² is hydrogen, C₁-C₆alkyl, C₁-C₆alkoxy, C₁-C₆haloalkyl,C₁-C₆haloalkoxy, aryl, or (aryl)alkyl;

each instance of R³ independently is hydroxy, sulfate, nitro, amino,halogen, cyano, C₁-C₄alkyl, C₁-C₄alkoxy, C₃-C₇cycloalkyl, mono- anddi-(C₁-C₄alkyl)amino, C₂-C₆alkoxycarbonyl, C₂-C₆alkanoyl,C₁-C₂haloalkyl, C₁-C₂haloalkoxy, phenyl, pyridyl, heterocycloalkyl,alkylcarboxamide, C₂-C₄alkenyl, or C₂-C₄alkynyl;

n is 0, 1, or 2;

m is 0 or 1;

Q is a bond or a C₁-C₆ hydrocarbon linking group comprising 0, 1, or 2heteroatoms chosen from O, S, or NR⁴, and wherein the linking group issubstituted by 0, 1, 2, or 3 substituents independently chosen fromhydroxy, sulfate, nitro, amino, cyano, halogen, C₁-C₄alkyl,C₃-C₇cycloalkyl, C₁-C₄alkoxy, mono- and di-(C₁-C₄alkyl)amino,C₂-C₆alkoxycarbonyl, C₂-C₆alkanoyl, C₁-C₂haloalkyl, C₁-C₂haloalkoxy, oroxo;

R⁴ is hydrogen, C₁-C₆alkyl, or C₁-C₆haloalkyl;

Y is —(C═O)NH—N═CH—,

—(C═O)NH—,

—NH(C═O)—,

—(C═O)—,

—O(C═O)—

—O(C═O)O—,

—NH(C═O)NH—,

—NH(C═O)O—,

—(C═O)NH—

or

—(C═O)—;

Z is a bond or a C₁-C₃ hydrocarbon linking group comprising 0, 1, or 2heteroatoms chosen from O, S, or NR⁴, and wherein the linking group issubstituted by 0, 1, 2, or 3 substituents independently chosen fromhydroxy, amino, cyano, halogen, C₁-C₄alkyl, C₃-C₇cycloalkyl,C₁-C₄alkoxy, mono- and di-(C₁-C₄alkyl)amino, C₂-C₆alkoxycarbonyl,C₂-C₆alkanoyl, C₁-C₂haloalkyl, C₁-C₂haloalkoxy, or oxo;

Ar is aryl or heteroaryl, substituted with 0, 1, 2, or 3 substituentsindependently chosen from hydroxy, sulfate, nitro, amino, cyano,halogen, C₁-C₄alkyl, C₃-C₇cycloalkyl, C₁-C₄alkoxy, mono- anddi-(C₁-C₄alkyl)amino, C₂-C₆alkoxycarbonyl, C₂-C₆alkanoyl,C₁-C₂haloalkyl, C₁-C₂haloalkoxy, phenyl, pyridyl, heterocycloalkyl,alkylcarboxamide, C₂-C₄alkenyl, or C₂-C₄alkynyl, and

the dashed line in the G structures is a single or double bond.

In another aspect, a method of treating a subject in need of treatmentfor a bacterial infection, comprises administering to the subject aneffective amount of a cell division inhibitor as defined above.

In yet another aspect, a method of inhibiting bacterial growth comprisescontacting the bacteria with a cell division inhibitor as defined abovein an amount sufficient to inhibit bacterial growth.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows the in vivo localization of FtsZ-GFP at the division planeand a schematic of FtsZ assembly and the concentration gradient of MipZwhich concentrates FtsZ assembly at the division plane in Caulobactercrescentus.

FIG. 2 is a schematic of the assay used to identify inhibitors of MipZ.

FIG. 3 shows that compound 1 inhibits septation during reproduction inC. crescentus and Escherichia coli.

FIG. 4 shows that compound 1 rescues cell elongation caused by MipZoverexpression.

FIGS. 5 and 6 show that compound 1 rescues division defects in a C.crescentus ΔzapA strain.

FIG. 7 shows viability of C. crescentus after exposure to kanamycin andcompound 1.

FIG. 8 shows that compound 1 perturbs the localization of several Ftsproteins, including FtsB, FtsL, FtsI, and FtsK, in C. crescentus.

FIG. 9 shows that compound 1 perturbs the assembly of division proteinsin E. coli cells.

FIG. 10 shows that the inhibitory effect of compound 1 on cell divisionis reversible.

The above-described and other features will be appreciated andunderstood by those skilled in the art from the following detaileddescription, drawings, and appended claims.

DETAILED DESCRIPTION

Described herein are novel inhibitors of cell division and their use totreat bacterial infections. Bacterial cells reproduce by coordinatinggrowth, DNA replication, and division into two daughter cells. Thephysical separation of two cells involves a bacterial tubulin homologFtsZ. Without being held to theory, it is believed that FtsZ polymerswork together to provide a constricting force in a dividing cell andalso serve as a scaffold to recruit other proteins necessary fordivision.

In C. crescentus cells, the mechanism of accurately placing FtsZ in timeand space in the cell involves an ATPase, MipZ. (FIG. 1) The ATP-boundform of MipZ promotes depolymerization of FtsZ filaments by increasingthe GTP hydrolysis rate of FtsZ. In addition to its inhibition of FtsZ,MipZ binds to nucleoproteins near the origin of the chromosome andestablishes an asymmetric polar gradient. The gradient becomes bipolar(i.e., symmetric) when the cell undergoes chromosome replication toplace two origins at opposite poles. This bipolar gradient of MipZpositions the division at the mid-cell: FtsZ is localized at themid-cell, where the concentration of the inhibitory gradient of MipZ isthe lowest. Thus, MipZ coordinates chromosome segregation and the onsetof cell division both spatially and temporally such that FtsZ assemblesat the mid-cell after the segregation of the chromosomes. Because of therelationship between FtsZ and MipZ, a coupling assay and a fluorescencepolarization assay of MipZ ATPase activity were used to screen compoundsfor their ability to inhibit cell division. (FIG. 2)

From a high-throughput screen at the Keck Small Molecule Facility at theUniversity of Wisconsin, a small molecule inhibitor of cell division inthe model bacterium Caulobacter crescentus, compound 1, was identified.The compound is toxic to C. crescentus and has a minimum inhibitoryconcentration of 5 μM. Compound 1 and its analogs are a new class ofantimicrobial compounds.

Several lines of evidence suggest that compound 1 and its analogsinhibit cell division specifically: 1) Cells treated with compound 1exhibit a cell division defect similar to mutant cells that overexpressFtsZ. 2) The overexpression of an inhibitor of FtsZ polymerization(MipZ) inhibits the initiation of division and causes cells to grow intolong filaments. The addition of compound 1 relieves this phenotype bymaking it possible for cells to divide in the presence of excess MipZ.3) Knocking out a protein (ZapA) that stabilizes FtsZ causes celldivision to occur at random positions along the cell and leads to anincrease in the average and standard deviation of cell length. Treatingthe knock-out strain with compound 1 attenuates this increase andreturns the cell length distribution back to normal. 4) Treatment withcompound 1 caused incomplete constrictions in dividing cells of C.crescentus and E. coli, although cells resume and finish the divisionprocess when the compound is washed away. 5) Compound 1 perturbs thelocalization of several fluorescently tagged Fts proteins, includingFtsB, FtsL, FtsI, and FtsK. The perturbation in the assembly of divisionproteins was also observed in E. coli cells.

Compound 1 has the following structure:

In one embodiment, the cell division inhibitor includes compounds andpharmaceutically acceptable salts of Formula I:

G-Q-Y-Z-Ar   (I)

wherein

G is

wherein each instance of A is independently CH or N provided that thetotal number of N is 0 or 1;

R¹ is hydrogen, hydroxy, amino, halogen, cyano, C₁-C₆alkoxy,C₁-C₆haloalkyl, C₁-C₆haloalkoxy, aryl, or (aryl)alkyl;

X¹ is N, CR², O, or S;

X² is O, S, or NR⁴;

R² is hydrogen, C₁-C₆alkyl, C₁-C₆alkoxy, C₁-C₆haloalkyl,C₁-C₆haloalkoxy, aryl, or (aryl)alkyl;

each instance of R³ independently is hydroxy, sulfate, nitro, amino,halogen, cyano, C₁-C₄alkyl, C₁-C₄alkoxy, C₃-C₇cycloalkyl, mono- anddi-(C₁-C₄alkyl)amino, C₂-C₆alkoxycarbonyl, C₂-C₆alkanoyl,C₁-C₂haloalkyl, C₁-C₂haloalkoxy, phenyl, pyridyl, heterocycloalkyl,alkylcarboxamide, C₂-C₄alkenyl, or C₂-C₄alkynyl;

n is 0, 1, or 2;

m is 0 or 1;

Q is a bond or a C₁-C₆ hydrocarbon linking group comprising 0, 1, or 2heteroatoms chosen from O, S, or NR⁴, and wherein the linking group issubstituted by 0, 1, 2, or 3 substituents independently chosen fromhydroxy, sulfate, nitro, amino, cyano, halogen, C₁-C₄alkyl,C₃-C₇cycloalkyl, C₁-C₄alkoxy, mono- and di-(C₁-C₄alkyl)amino,C₂-C₆alkoxycarbonyl, C₂-C₆alkanoyl, C₁-C₂haloalkyl, C₁-C₂haloalkoxy, oroxo;

R⁴ is hydrogen, C₁-C₆alkyl, or C₁-C₆haloalkyl;

Y is —(C═O)NH—N═CH—,

—(C═O)NH—,

—NH(C═O)—,

—(C═O)O—,

—O(C═O)—

—O(C═O)O—,

—NH(C═O)NH—,

—NH(C═O)O—,

—O(C═O)NH—

or

—(C═O)—;

Z is a bond or a C₁-C₃ hydrocarbon linking group comprising 0, 1, or 2heteroatoms chosen from O, S, or NR⁴, and wherein the linking group issubstituted by 0, 1, 2, or 3 substituents independently chosen fromhydroxy, amino, cyano, halogen, C₁-C₄alkyl, C₃-C₇cycloalkyl,C₁-C₄alkoxy, mono- and di-(C₁-C₄alkyl)amino, C₂-C₆alkoxycarbonyl,C₂-C₆alkanoyl, C₁-C₂haloalkyl, C₁-C₂haloalkoxy, or oxo;

Ar is aryl or heteroaryl, substituted with 0, 1, 2, or 3 substituentsindependently chosen from hydroxy, sulfate, nitro, amino, cyano,halogen, C₁-C₄alkyl, C₃-C₇cycloalkyl, C₁-C₄alkoxy, mono- anddi-(C₁-C₄alkyl)amino, C₂-C₆alkoxycarbonyl, C₂-C₆alkanoyl,C₁-C₂haloalkyl, C₁-C₂haloalkoxy, phenyl, pyridyl, heterocycloalkyl,alkylcarboxamide, C₂-C₄alkenyl, or C₂-C₄alkynyl; and

the dashed line in the G structures is a single or double bond.

Within this embodiment, R¹ is hydrogen, fluoro, C₁-C₃alkyl, C₁-C₃alkoxy,C₁-C₃haloalkyl (e.g. fluoroalkyl), C₁-C₃haloalkoxy, or aryl, morespecifically R¹ is hydrogen, C₁-C₂alkyl, C₁-C₂alkoxy, C₁-C₂haloalkyl, orC₁-C₂haloalkoxy, and yet more specifically R¹ is methyl ortrifluoromethyl.

Further within this embodiment, X¹ is N.

Still further within this embodiment, each instance of R³ independentlyis hydroxy, sulfate, nitro, halogen, C₁-C₂alkyl, C₁-C₂alkoxy,C₃-0₅cycloalkyl, mono- and di-(C₁-C₂alkyl)amino, C₂-C₄alkoxycarbonyl,C₁-C₂haloalkyl, or C₁-C₂haloalkoxy.

Within this embodiment Q is a C₁-C₃ hydrocarbon linking groupsubstituted by 0, 1, 2, or 3 substituents independently chosen fromhydroxy, amino, halogen (specifically fluoro), C₁-C₂alkyl,C₃-C₅cycloalkyl, C₁-C₂alkoxy, mono- and di-(C₁-C₂alkyl)amino,C₂-C₄alkoxycarbonyl, C₁-C₂haloalkyl (specifically fluoroalkyl),C₁-C₂haloalkoxy (specifically fluoroalkoxy), or oxo.

Further within this embodiment, Y is —(C═O)NH—N═CH—,

—(C═O)NH—,

—NH(C═O)NH—,

—NH(C═O)O—, or

—O(C═O)NH—.

Also within this embodiment, Z is a bond.

Furthermore, within this embodiment, Ar is aryl substituted with 1 or 2substituents independently chosen from hydroxy, amino, cyano, halogen(specifically fluoro), C₁-C₄alkyl, C₃-C₇cycloalkyl, C₁-C₄alkoxy, mono-and di-(C₁-C₄alkyl)amino, C₂-C₆alkoxycarbonyl, C₁-C₂haloalkyl(specifically fluoroalkyl), or C₁-C₂haloalkoxy (specificallyfluoroalkoxy).

In another embodiment, the inhibitor includes compounds andpharmaceutically acceptable salts of Formula Ia:

wherein

R¹, X¹, R³, n, Q, and Ar are as previously defined. In one embodiment,Ar is substituted naphthalene, specifically substituted with a hydroxygroup or a methoxy group, or Ar is a substituted phenyl specificallysubstituted with a hydroxy group. In one embodiment, R¹ is H, CF₃ orCH₃. In one embodiment, Q is C₂alkyl.

In specific embodiments, the cell division inhibitor is compound 1 orits trifluoro analog, compound 6:

Additional analogs of compound 1 are compounds 7-9:

In certain situations, the compounds of Formulae I and Ia may containone or more asymmetric elements such as stereogenic centers, stereogenicaxes and the like, e.g., asymmetric carbon atoms, so that the compoundscan exist in different stereoisomeric forms. These compounds can be, forexample, racemates or optically active forms. For compounds with two ormore asymmetric elements, these compounds can additionally be mixturesof diastereomers. For compounds having asymmetric centers, it should beunderstood that all of the optical isomers and mixtures thereof areencompassed. In addition, compounds with double bonds may occur in Z-and E-forms, with all isomeric forms of the compounds being included inthe present disclosure. In these situations, the single enantiomers,i.e., optically active forms, can be obtained by asymmetric synthesis,synthesis from optically pure precursors, or by resolution of theracemates. Resolution of the racemates can also be accomplished, forexample, by conventional methods such as crystallization in the presenceof a resolving agent, or chromatography, using, for example a chiralHPLC column.

The term “substituted”, as used herein, means that any one or morehydrogens on the designated atom or group is replaced with a selectionfrom the indicated group, provided that the designated atom's normalvalence is not exceeded. When a substituent is oxo (i.e., =O), then 2hydrogens on the atom are replaced. When aromatic moieties aresubstituted by an oxo group, the aromatic ring is replaced by thecorresponding partially unsaturated ring. For example a pyridyl groupsubstituted by oxo is a pyridone. Combinations of substituents and/orvariables are permissible only if such combinations result in stablecompounds or useful synthetic intermediates. A stable compound or stablestructure is meant to imply a compound that is sufficiently robust tosurvive isolation from a reaction mixture, and subsequent formulationinto an effective therapeutic agent.

A dash (“-”) that is not between two letters or symbols is used toindicate a point of attachment for a substituent. For example, —COOH isattached through the carbon atom.

As used herein, “alkyl” is intended to include both branched andstraight-chain saturated aliphatic hydrocarbon groups, having thespecified number of carbon atoms. Thus, the term C₁-C₆alkyl as usedherein includes alkyl groups having from 1 to about 6 carbon atoms. WhenC₀-C_(n) alkyl is used herein in conjunction with another group, forexample, phenylC₀-C₄alkyl, the indicated group, in this case phenyl, iseither directly bound by a single covalent bond (C₀), or attached by analkyl chain having the specified number of carbon atoms, in this casefrom 1 to about 2 carbon atoms. Examples of alkyl include, but are notlimited to, methyl, ethyl, n-propyl, isopropyl, n-butyl, t-butyl,n-pentyl, and sec-pentyl.

“Alkenyl” as used herein, indicates hydrocarbon chains of either astraight or branched configuration comprising one or more unsaturatedcarbon-carbon bonds, which may occur in any stable point along thechain, such as ethenyl and propenyl.

“Alkynyl” as used herein, indicates hydrocarbon chains of either astraight or branched configuration comprising one or more triplecarbon-carbon bonds that may occur in any stable point along the chain,such as ethynyl and propynyl.

“Alkoxy” represents an alkyl group as defined above with the indicatednumber of carbon atoms attached through an oxygen bridge. Examples ofalkoxy include, but are not limited to, methoxy, ethoxy, n-propoxy,propoxy, n-butoxy, 2-butoxy, t-butoxy, n-pentoxy, 2-pentoxy, 3-pentoxy,isopentoxy, neopentoxy, n-hexoxy, 2-hexoxy, 3-hexoxy, and3-methylpentoxy.

“Alkanoyl” indicates an alkyl group as defined above, attached through aketo (—(C═O)—) bridge. Alkanoyl groups have the indicated number ofcarbon atoms, with the carbon of the keto group being included in thenumbered carbon atoms. For example a C₂alkanoyl group is an acetyl grouphaving the formula CH₃(C═O)—.

The term “alkoxycarbonyl” indicates an alkoxy group, as defined above,having the indicated number of carbon atoms, attached through a ketolinkage. The carbon of the keto linker is not included in the numbering,thus a C₂alkoxycarbonyl has the formula CH₃CH₂O(C═O)—.

The term “alkylcarboxamide” indicates an alkyl group, as defined above,having the indicated number of carbon atoms, attached through acarboxamide linkage, i.e., a —CONH₂ linkage, where one or both of theamino hydrogens is replaced by an alkyl group. Alkylcarboxamide groupsmay be mono- or di-alkylcarboxamide groups, such an ethylcarboxamide ordimethylcarboxamide.

As used herein, the term “mono- or di-alkylamino” indicates secondary ortertiary alkyl amino groups, wherein the alkyl groups are as definedabove and have the indicated number of carbon atoms. The point ofattachment of the alkylamino group is on the nitrogen. Examples of mono-and di-alkylamino groups include ethylamino, dimethylamino, andmethyl-propyl-amino.

As used herein, the term “aryl” indicates aromatic groups containingonly carbon in the aromatic ring or rings. Such aromatic groups may befurther substituted with carbon or non-carbon atoms or groups. Typicalaryl groups contain 1 to 3 separate, fused, or pendant rings and from 6to about 18 ring atoms, without heteroatoms as ring members. Whereindicated aryl groups may be substituted. Such substitution may includefusion to a 5 to 7-membered saturated cyclic group that optionallycontains 1 or 2 heteroatoms independently chosen from N, O, and S, toform, for example, a 3,4-methylenedioxy-phenyl group. Aryl groupsinclude, for example, phenyl, naphthyl, including 1-naphthyl and2-naphthyl, and bi-phenyl.

In the term “(aryl)alkyl”, aryl and alkyl are as defined above, and thepoint of attachment is on the alkyl group. This term encompasses, but isnot limited to, benzyl, phenylethyl, and piperonyl. Likewise, in theterm (aryl)carbhydryl, aryl and carbhydryl are as defined above and thepoint of attachment is on the carbhydryl group, for example aphenylpropen-1-yl group.

“Carbhydryl” as used herein, includes both branched and straight-chainhydrocarbon groups, which are saturated or unsaturated, having thespecified number of carbon atoms.

“Cycloalkyl” as used herein, indicates saturated hydrocarbon ringgroups, having the specified number of carbon atoms, usually from 3 toabout 8 ring carbon atoms, or from 3 to about 7 carbon atoms. Examplesof cycloalkyl groups include cyclopropyl, cyclobutyl, cyclopentyl, orcyclohexyl as well as bridged or caged saturated ring groups such asnorbornane or adamantane.

“Haloalkyl” indicates both branched and straight-chain saturatedaliphatic hydrocarbon groups having the specified number of carbonatoms, substituted with 1 or more halogen atoms, generally up to themaximum allowable number of halogen atoms. Examples of haloalkylinclude, but are not limited to, trifluoromethyl, difluoromethyl,2-fluoroethyl, and penta-fluoroethyl.

“Haloalkoxy” indicates a haloalkyl group as defined above attachedthrough an oxygen bridge.

“Halo” or “halogen” as used herein refers to fluoro, chloro, bromo, oriodo.

As used herein, “heteroaryl” indicates a stable 5- to 7-memberedmonocyclic or 7- to 10-membered bicyclic heterocyclic ring whichcontains at least 1 aromatic ring that contains from 1 to 4, orpreferably from 1 to 3, heteroatoms chosen from N, O, and S, withremaining ring atoms being carbon. When the total number of S and Oatoms in the heteroaryl group exceeds 1, these heteroatoms are notadjacent to one another. It is preferred that the total number of S andO atoms in the heteroaryl group is not more than 2. Examples ofheteroaryl groups include, but are not limited to, pyridyl, indolyl,pyrimidinyl, pyridizinyl, pyrazinyl, imidazolyl, oxazolyl, furanyl,thiophenyl, thiazolyl, triazolyl, tetrazolyl, isoxazolyl, quinolinyl,pyrrolyl, pyrazolyl, and 5,6,7,8-tetrahydroisoquinoline. In the term“heteroarylalkyl,” heteroaryl and alkyl are as defined above, and thepoint of attachment is on the alkyl group. This term encompasses, but isnot limited to, pyridylmethyl, thiophenylmethyl, and pyrrolyl(1-ethyl).

The term “heterocycloalkyl” is used to indicate saturated cyclic groupscontaining from 1 to about 3 heteroatoms chosen from N, O, and S, withremaining ring atoms being carbon. Heterocycloalkyl groups have from 3to about 8 ring atoms, and more typically have from 5 to 7 ring atoms. AC₂-C₇heterocycloalkyl group contains from 2 to about 7 carbon ring atomsand at least one ring atom chosen from N, O, and S. Examples ofheterocycloalkyl groups include morpholinyl, piperazinyl, piperidinyl,and pyrrolidinyl groups.

“Pharmaceutically acceptable salts” includes derivatives of thedisclosed compounds wherein the parent compound is modified by making anacid or base salt thereof, and further refers to pharmaceuticallyacceptable solvates of such compounds and such salts. Examples ofpharmaceutically acceptable salts include, but are not limited to,mineral or organic acid salts of basic residues such as amines; alkalior organic salts of acidic residues such as carboxylic acids; and thelike. The pharmaceutically acceptable salts include the conventionalsalts and the quaternary ammonium salts of the parent compound formed,for example, from inorganic or organic acids. For example, conventionalacid salts include those derived from inorganic acids such ashydrochloric, hydrobromic, sulfuric, sulfamic, phosphoric, nitric andthe like; and the salts prepared from organic acids such as acetic,propionic, succinic, glycolic, stearic, lactic, malic, tartaric, citric,ascorbic, pamoic, maleic, hydroxymaleic, phenylacetic, glutamic,benzoic, salicylic, mesylic, esylic, besylic, sulfanilic,2-acetoxybenzoic, fumaric, toluenesulfonic, methanesulfonic, ethanedisulfonic, oxalic, isethionic, HOOC—(CH₂)_(n)—COOH where n is 0-4, andthe like. The pharmaceutically acceptable salts of the present inventioncan be synthesized from a parent compound that contains a basic oracidic moiety by conventional chemical methods. Generally, such saltscan be prepared by reacting free acid forms of these compounds with astoichiometric amount of the appropriate base (such as Na, Ca, Mg, or Khydroxide, carbonate, bicarbonate, or the like), or by reacting freebase forms of these compounds with a stoichiometric amount of theappropriate acid. Such reactions are typically carried out in water orin an organic solvent, or in a mixture of the two. Generally,non-aqueous media like ether, ethyl acetate, ethanol, isopropanol, oracetonitrile are preferred, where practicable.

In one aspect, provided herein are methods of treating a subject in needof treatment for a bacterial infection, comprising administering to theindividual a cell division inhibitor (also referred to herein as anantimicrobial compound) as described herein. The bacteria causing theinfection can be Gram-negative or Gram-positive bacteria, specificallyGram-negative bacteria. Gram-negative bacteria include Escherchia coli,Caulobacter crescentus, Pseudomonas aeruginosa, Agrobacteriumtumefaciens, Branhamella catarrhalis, Citrobacter diversus, Enterobacteraerogenes, Klebsiella pneumoniae, Proteus mirabilis, Salmonellatyphimurium, Neisseria meningitidis, Serratia marcescens, Shigellasonnei, Shigella boydii, Vibrio cholera, Neisseria gonorrhoeae,Acinetobacter baumannii, Salmonella enteriditis, Fusobacteriumnucleatum, Veillonella parvula, Bacteroides forsythus, Actinobacillusactinomycetemcomitans, Aggregatibacter actinomycetemcomitans,Porphyromonas gingivalis, Helicobacter pylori, Francisella tularensis,Yersinia pestis, Morganella morganii, Edwardsiella tarda, Acinetobacterbaumannii and Haemophilus influenzae. In another embodiment, thebacteria are Gram-positive bacteria. Gram-positive bacteria includespecies of Bacillus, Listeria, Staphylococcus, Streptococcus,Enterococcus, Enterobacter, Corynebacterium, Propionibacterium andClostridium. Specific Gram-positive bacteria include Staphylococcusaureus, Staphylococcus epidermidis, Enterococcus faecium, and Bacillussubtilis. In a specific embodiment, the bacteria are one or more drugresistant bacteria.

In another aspect, a method of inhibiting bacterial growth comprisescontacting the bacteria with an antimicrobial compound as describedherein. Methods of inhibiting bacteria include methods useful fortreatment of a subject (human or veterinary) and also include methodsuseful for inhibiting bacteria outside of a subject, such as use forsterilization and disinfection.

The antimicrobial compounds and compositions may be administeredprophylactically, chronically, or acutely. For example, such compoundsmay be administered prophylactically to patients known to be prone tobacterial infections, or who are known to have been exposed topotentially infectious agents. The compounds may also be administeredprophylactically to patients suffering other conditions, such as AIDS orother immune-system-suppressing conditions, that render them susceptibleto opportunistic infections. In addition to the prevention of suchinfections, chronic administration of the antimicrobial compounds willtypically be indicated in treating refractory conditions, such aspersistent infection by multiple drug-resistant strains of bacteria.Acute administration of the antimicrobial compounds is indicated totreat, for example, those subjects presenting with classical indicationsof bacterial infection.

As used herein, “contacting” means that a compound is provided such thatit is capable of making physical contact with another element, such as amicroorganism, a microbial culture or a substrate. In anotherembodiment, the term “contacting” means that the compound is introducedinto a subject receiving treatment, and the compound is allowed to comein contact in vivo. Thus, contacting can include administration of acompound, that is, introducing the compound into the body, such as intothe systemic circulation. Administration routes include but are notlimited to, rectal, oral; buccal, sublingual, pulmonary, transdermal,transmucosal, as well as subcutaneous, intraperitoneal, intravenous, andintramuscular injection.

Since the antimicrobial compounds are antibacterially active and inhibitbacterial growth, they are also of use in treating bacterialcontamination of a substrate, such as hospital instruments or worksurfaces. In order to treat a contaminated substrate, the compounds maybe applied to the site of such contamination in an amount sufficient toinhibit bacterial growth.

In certain embodiments, the compounds are administered to a patient orsubject. A “patient” or “subject”, used equivalently herein, meansmammals and non-mammals. “Mammals” means a member of the class Mammaliaincluding, but not limited to, humans, non-human primates such aschimpanzees and other apes and monkey species; farm animals such ascattle, horses, sheep, goats, and swine; domestic animals such asrabbits, dogs, and cats; laboratory animals including rodents, such asrats, mice, and guinea pigs; and the like. Examples of non-mammalsinclude, but are not limited to, birds, and the like. The term “subject”does not denote a particular age or sex.

The phrase “effective amount,” as used herein, means an amount of anagent which is sufficient enough to significantly and positively modifysymptoms and/or conditions to be treated (e.g., provide a positiveclinical response). The effective amount of an active ingredient for usein a pharmaceutical composition will vary with the particular conditionbeing treated, the severity of the condition, the duration of thetreatment, the nature of concurrent therapy, the particular activeingredient(s) being employed, the particular pharmaceutically-acceptableexcipient(s)/carrier(s) utilized, and like factors within the knowledgeand expertise of the attending physician. In general, the use of theminimum dosage that is sufficient to provide effective therapy ispreferred. Patients may generally be monitored for therapeuticeffectiveness using assays suitable for the condition being treated orprevented, which will be familiar to those of ordinary skill in the art.

The phrase “inhibitory amount”, as used herein, means an amount of anagent (a compound or composition) which is sufficient to reduce thelevel or activity of bacterial infection to a statistically significantlesser value as compared to when the agent is not present.

The amount of compound effective for any indicated condition will, ofcourse, vary with the individual subject being treated and is ultimatelyat the discretion of the medical or veterinary practitioner. The factorsto be considered include the condition being treated, the route ofadministration, the nature of the formulation, the subject's bodyweight, surface area, age and general condition, and the particularcompound to be administered. In general, a suitable effective dose is inthe range of about 0.1 to about 500 mg/kg body weight per day,preferably in the range of about 5 to about 350 mg/kg per day. The totaldaily dose may be given as a single dose, multiple doses, e. g., two tosix times per day, or by intravenous infusion for a selected duration.Dosages above or below the range cited above may be administered to theindividual patient if desired and necessary.

As used herein, “pharmaceutical composition” means therapeuticallyeffective amounts of the compound together with a pharmaceuticallyacceptable excipient, such as diluents, preservatives, solubilizers,emulsifiers, and adjuvants. As used herein “pharmaceutically acceptableexcipients” are well known to those skilled in the art.

Tablets and capsules for oral administration may be in unit dose form,and may contain conventional excipients such as binding agents, forexample syrup, acacia, gelatin, sorbitol, tragacanth, orpolyvinyl-pyrrolidone; fillers for example lactose, sugar, maize-starch,calcium phosphate, sorbitol or glycine; tabletting lubricant, forexample magnesium stearate, talc, polyethylene glycol or silica;disintegrants for example potato starch, or acceptable wetting agentssuch as sodium lauryl sulphate. The tablets may be coated according tomethods well known in normal pharmaceutical practice. Oral liquidpreparations may be in the form of, for example, aqueous or oilysuspensions, solutions, emulsions, syrups or elixirs, or may bepresented as a dry product for reconstitution with water or othersuitable vehicle before use. Such liquid preparations may containconventional additives such as suspending agents, for example sorbitol,syrup, methyl cellulose, glucose syrup, gelatin hydrogenated ediblefats; emulsifying agents, for example lecithin, sorbitan monooleate, oracacia; non-aqueous vehicles (which may include edible oils), forexample almond oil, fractionated coconut oil, oily esters such asglycerine, propylene glycol, or ethyl alcohol; preservatives, forexample methyl or propyl p-hydroxybenzoate or sorbic acid, and ifdesired conventional flavoring or coloring agents.

For topical application to the skin, the drug may be made up into acream, lotion or ointment. Cream or ointment formulations which may beused for the drug are conventional formulations well known in the art.Topical administration includes transdermal formulations such aspatches.

For topical application to the eye, the inhibitor may be made up into asolution or suspension in a suitable sterile aqueous or non aqueousvehicle. Additives, for instance buffers such as sodium metabisulphiteor disodium edeate; preservatives including bactericidal and fungicidalagents such as phenyl mercuric acetate or nitrate, benzalkonium chlorideor chlorhexidine, and thickening agents such as hypromellose may also beincluded.

The active ingredient may also be administered parenterally in a sterilemedium, either subcutaneously, or intravenously, or intramuscularly, orintrasternally, or by infusion techniques, in the form of sterileinjectable aqueous or oleaginous suspensions. Depending on the vehicleand concentration used, the drug can either be suspended or dissolved inthe vehicle. Advantageously, adjuvants such as a local anaesthetic,preservative and buffering agents can be dissolved in the vehicle.

Pharmaceutical compositions may conveniently be presented in unit dosageform and may be prepared by any of the methods well known in the art ofpharmacy. The term “unit dosage” or “unit dose” means a predeterminedamount of the active ingredient sufficient to be effective for treatingan indicated activity or condition. Making each type of pharmaceuticalcomposition includes the step of bringing the active compound intoassociation with a carrier and one or more optional accessoryingredients. In general, the formulations are prepared by uniformly andintimately bringing the active compound into association with a liquidor solid carrier and then, if necessary, shaping the product into thedesired unit dosage form.

The antimicrobial compounds may also be administered in combination withan additional active agent, such as, for example, an inhibitor ofbacterial efflux. Efflux pumps are proteins that unidirectionally removeantibiotics from cytoplasmic compartments, and are considered to be amechanism of antibacterial resistance. Bacterial efflux inhibitorsinclude chalcone compounds as disclosed in WO 11/075136, the polybasiccompounds disclosed in WO 10/054102, the quaternary alkyl ammoniumfunctional compounds disclosed in WO 08/141012, the compounds disclosedin WO 05/007162, the substituted polyamines of WO 04/062674, which areincorporated herein by reference in their entirety.

In another embodiment, the antimicrobial compounds of formula 1 can beadministered with a second antibiotic. Exemplary second antibioticsinclude, for example, glycopeptides (e.g, vancomycin or teicoplanin);penicillins, such as amdinocillin, ampicillin, amoxicillin, azlocillin,bacampicillin, benzathine penicillin G, carbenicillin, cloxacillin,cyclacillin, dicloxacillin, methicillin, mezlocillin, nafcillin,oxacillin, penicillin G, penicillin V, piperacillin, and ticarcillin;cephalosporins, such as cefadroxil, cefazolin, cephalexin, cephalothin,cephapirin, cephradine, cefaclor, cefamandole, cefonicid, ceforanide,cefoxitin, and cefuroxime, cefoperazone, cefotaxime, cefotetan,ceftazidime, ceftizoxime, ceftriaxone, and moxalactam; carbapenems suchas imipenem; monobactams such as aztreonam; tetracyclines such asdemeclocycline, tigilcycline, doxycycline, methacycline, minocycline,and oxytetracycline; aminoglycosides such as amikacin, gentamicin,kanamycin, neomycin, netilmicin, paromomycin, spectinomycin,streptomycin, and tobramycin; polymyxins such as colistin,colistimathate, and polymyxin B, and erythromycins and lincomycins andalso sulfonamides such as sulfacytine, sulfadiazine, sulfisoxazole,sulfamethoxazole, sulfamethizole, and sulfapyridine; trimethoprim,quinolones, novobiocin, pyrimethamine, and rifampin; and combinationsthereof.

The invention is further illustrated by the following non-limitingexamples.

EXAMPLES Example 1 Selection of Cell Division Inhibitors

In vitro ATPase screen with purified recombinant MipZ: The assays usedfor screening compounds were a coupling assay and a fluorescencepolarization assay of MipZ ATPase activity. Recombinant MipZ for the invitro screen was purified as described in Thanbichler and Shapiro (Cell,2006). Two ATPase assays were used to screen three small moleculelibraries (a total of 43,400 compounds) at the University of WisconsinCarbone Cancer Center. One assay utilized pyruvate kinase and lacticdehydrogenase as coupling enzymes and phosphoenolpyruvate and NADH,respectively, as their substrates. A solution of coupling enzymes, theirsubstrates, Triton X, and MipZ was aliquoted (22.3 μL per well) into384-well black plates using a Biomek FX liquid handler (BeckmanCoulter). Plates were briefly centrifuged to pull liquids to the bottomof the wells. Pin tools were used to deliver 0.2 μL of a unique smallmolecule to each well from a stock solution (10 mM in DMSO) from thechemical libraries. The first two columns of each plate were reservedfor controls and did not receive compounds from the libraries. UsingBiotek Fill, ATP hydrolysis was initiated by adding a solution of ATP toeach well, with the exception of those in the first column of eachplate. The final concentrations of the assay components were as follows:0.01% Triton X, 1 mM phosphoenolpyruvate, 0.3 mM NADH, 3 U/mL pyruvatekinase, 3 U/mL lactic dehydrogenase, 7.5 μM MipZ, and 1 mM ATP in abuffered solution of 50 mM Tris-HCl, 50 mM KCl, and 10 mM MgCl₂. Plateswere gently vortexed to mix the solution and incubated for three hoursat 30° C. After incubation, the fluorescence emission from NADH wasmeasured using a Tecan Safire II™ (λ_(ex)=340/35 nm; λ_(em)=460/10 nm).The fluorescence intensity in the control wells was used to calculatethe Z-factor; the minimum Z-factor for all plates was 0.7. The couplingenzyme assay was used to screen compounds from the Maybridge and LifeChemicals libraries. Compounds that inhibited ≧60% of ATP hydrolysiscompared with the positive control were identified as hits, and theywere screened using a secondary assay to eliminate compounds that targetcoupling enzymes. The secondary assay consisted of the same reactioncomponents as the primary assay with two exceptions: (1) MipZ wasomitted, and (2) ATP was replaced with ADP. The compounds that did notinhibit coupling enzymes were then checked for intrinsic fluorescence atthe specified wavelengths used for NADH and retested for their activityagainst MipZ in vitro.

In addition to the coupling enzyme assay, a fluorescence polarization(FP) assay was used to monitor the ATPase activity of MipZ in vitro.(FIG. 2) Reaction conditions and component concentrations were same asin the coupling enzyme assay unless otherwise noted. The FP assayutilized anti-ADP antibodies and Alexa 633-labeled ADP. TheTranscreener® ADP² FP assay kit was purchased from Bell Brook Labs. Asolution of MipZ was aliquoted into plates (10 μL per well), and thereaction was initiated by the addition of ATP (1 μL of 5 mM stocksolution per well). After three hours, 10 μL of ADP detection mix (541μg/mL of antibody) was added to each well, and the plates were furtherincubated for 1 hr at RT. The wavelengths used for FP measurements were635 nm for excitation and 670/20 nm for emission. The Z-factor for theFP assay was ≧0.7. The FP assay was used to screen compounds from theLife Chemicals library and the Spectrum Collection. Hits from the FPassay were checked for intrinsic fluorescence at the specifiedwavelengths used for the Alexa 633 probe and tested for any potentialinhibition of the anti-ADP antibody by repeating the assay in theabsence of MipZ.

Example 2 Screening of Hits for Antibacterial Activity

In vivo screen with a Caulobacter crecentus strain that expressesMipZ-YFP: Hits from the in vitro screens were tested for their activityin vivo. A C. crescentus strain (MT97) that expresses mipZ-yfp from thenative mipZ promoter was used. An overnight culture of MT97 was dilutedto an OD₆₀₀ of ˜0.1, and the diluted culture was further grown for atleast an hour prior to treatment with the compound. Compounds were mixedwith a solution of 1% agarose in M2G medium to achieve a finalconcentration of 20 μM. Cells were inoculated onto the surface of thecompound-containing agarose pad (1 μL inoculum per pad), and we observedthe cell morphology and localization of MipZ-YFP for a period of 24 hrs.In the time between microscopic observations, the inoculated pads werekept at 30° C. to promote growth.

As can be seen in FIG. 3, compound 1 inhibits septation duringreproduction in C. crescentus. The phenotype looks similar tooverexpression of FtsZ, suggesting that compound 1 affects celldivision.

Example 3 Determination of the MIC of Compound 1

Determination of the minimum inhibitory concentration (MIC): The MIC ofthe small molecule hits was determined using a macrodilution method. Allcultures were grown in M8 medium at 37° C., except for C. crescentus(strain CB15N) which was cultured in PYE media at 30° C. C. crescentusand E. coli cultures were incubated while shaking at 200 rpm. Pathogenicclinical strains were grown in static conditions. All cultures weregrown for 17 hrs.

The MIC of compound 1 for C. crescentus was 5 μM, while for E. coliΔtolC it was 13.5 μM, suggesting activity against Gram-negativebacteria. E. coli ΔtolC is a knockout of a component of the drug effluxpump, which results in a cell without an effective pump, and was used inplace of an efflux pump inhibitor in these experiments. The MIC of P190723 for E. coli reported in the literature is >180 μM. The MICs ofcompound 1 against pathogenic strains are 0.4 μM for Vibrio cholerae, 50μM for Shigella boydii, and 25 μM for Acinetobacter baumannii.

Example 4 Use of Microscopy to Visualize the Effects of Compound 1 onCell Division

Optical microscopy and image analysis: A Nikon Eclipse TE2000E invertedmicroscope with a Perfect Focus system and an encoded z-stage for phasecontrast and epifluorescence microscopy was used. To observe the effectof Compound 1 on cell division, freshly grown cells from an overnightculture were treated with the compound. Small aliquots (1-2 μL) of thecells dosed with Compound 1 were mounted on 1% agarose pads formicroscopy. To visualize FtsZ localization, MT 196 cells (C. crescentusCB15N P_(vanA)-ftsZ-yfp) were induced with vanilate (0.5 mM) for 1 hrprior to imaging. PSICIC, a MATLAB-based script, was used to measurecell lengths (n≧100) for the following strains of C. crescentus: CB15N,CB15N pMT182 (P_(xylX)-mipZ, Cm^(R)), and CB15N ΔzapA. The CB15N pMT182strain was treated with 0.2% xylose to induce overexpression of MipZ.For cells that could not be accurately detected by PSICIC, the celllength was manually traced in MetaMorph or ImageJ and the pixel traceswere converted to microns. GraphPad InStat was used for statisticalanalysis of cell length distributions.

As shown in FIG. 4, compound 1 rescues cell elongation caused by MipZoverexpression. MipZ overexpression inhibits FtsZ assembly at thedivision plate and causes filamentation. Compound 1 rescues thisphenotype suggesting that compound 1 stabilizes FtsZ filaments.

As shown in FIGS. 5 and 6, compound 1 also rescues division defects in aC. crescentus ΔzapA strain. ZapA stabilizes FtsZ in vivo and inducesFtsZ bundling in vitro. Deletion of ZapA leads to a heterogeneity incell length. Addition of compound 1 to a ΔzapA strain restores celllengths to near normal lengths.

Example 5 Viability of C. crescentus After Exposure to Antibiotics

Viable C. crescentus cells were counted after treatment with antibioticsto determine the toxicity effect of compound 1 on bacteria. Kanamycinwas used as a control since it is a known bacteriocidal agent. Anovernight culture of CB15N in PYE medium was diluted to an opticaldensity of 0.1 (λ=600 nm) and incubated further for 1.5 hrs. After theincubation, the culture was aliquoted into 15 mL conical tubes (1 mL ofculture per aliquot) and treated with antibiotics. The finalconcentration of the antibiotics was twice its minimum inhibitoryconcentration. Upon addition of antibiotics, the culture tubes werewrapped with aluminum foil and shaken at 250 rpm at 30° C. At every 30min, 100 μL was withdrawn from each aliquot and serially diluted fivetimes in M2G medium. 100 μL of the fifth dilution was spread on PYEplates, the plates were incubated for two days at 30° C., and the numberof colonies formed on the plates was counted. As shown in FIG. 7, thenumber of colonies increased over time due to cell growth and divisionwhen no antibiotics were added to the culture. On the other hand, abacteriocidal antibiotic, kanamycin, decreased the colony forming unitssince it induces cell death. Treating with compound 1 did notsignificantly alter the colony forming units over time, indicating thatit acts as a bacteriostatic agent to limit reproduction of bacteria.

Example 6 Compound 1 Perturbs the Localization of FtsB, FtsL, FtsK andFtsI in C. crescentus Cells

Strains of C. crescentus that express fluorescently-tagged Fts proteins(FtsB, FtsL, FtsK, and FtsI) were cultured overnight. The overnightcultures were diluted 10-fold and incubated for an hour at 30° C. priorto compound treatment. Cells were induced with xylose (0.3%) to triggerthe expression of fluorescently-tagged Fts proteins. After inducing withxylose for 45 min, cells were mounted on agarose pads and imaged asdescribed in Example 4.

To analyze changes in the localization of Fts proteins, cells in thelate division stage were selected for image analysis. At this stage ofthe cell cycle, cells have a visible constriction at the midcell, andthe Fts proteins localize to the constriction site. FIG. 8A (taken fromGoley et al., 2011, Molecular Microbiology) shows a schematic of variousdivision proteins that are recruited to the septum following thelocalization of FtsZ. Within the population of cells selected for avisible constriction, cells that have a single fluorescence focus of Ftsproteins were counted. FIG. 8B shows representative images for cellsexpressing Venus-FtsI. These cells have clear constrictions at themidcell as shown in brightfield images. In the fluorescence channel, thesignal from Venus-FtsI is localized at the septum in the DMSO sample. Incontrast, the fluorescence signal is more diffuse throughout the cellbody in the sample treated with compound 1. We calculated the percentageof cells with a fluorescence signal at the midcell, and found that thetreatment with compound 1 decreased the population of cells with amidcell localization of Fts proteins (FIG. 8C). The observed decrease inFts protein localization in the presence of compound 1 was statisticallysignificant when compared to the DMSO solvent control samples. Thisperturbation of division protein localization suggests that compound 1inhibits the proper assembly and maturation of the bacterial divisionmachinery.

Example 7 Co-Treatment with Compound 1 Decreases Cell Lysis andFilamentation Induced by Cephalexin

Cephalexin belongs to a family of β-lactam antibiotics that target thesynthesis of peptidoglycan cell wall. This compound binds to the activesite of FtsI to inhibit crosslinking of peptidoglycan at the septum.When cephalexin is added to E. coli cells, some cells undergo lysiswhile others elongate. A proposed mechanism for the cephalexin-inducedcell lysis is shown in FIG. 9A (adopted from Chung et al., 2009, PNAS).This model suggests that the inhibition of FtsI activity by cephalexindoes not affect the enzyme's ability to localize to the septum andrecruit downstream division proteins, including FtsN and amidases.Amidases readily cut the peptidoglycan at the septum to create holes forinserting new materials. When cephalexin is present, however, the holescreated by amidases cannot be repaired by FtsI. This inability to repairgaps in the peptidoglycan leads to cell lysis in cephalexin-treatedsamples. We utilized this mechanism of cephalexin-induced cell lysis totest whether the assembly of divisome is perturbed in the presence ofcompound 1. To this end, we used the E. coli ΔtolC construct to measurethe amount of cell lysis in the presence of compound 1 and cephalexin.The E. coli cells were grown overnight to stationary phase, and theovernight culture was diluted to an optical density of 0.1 (measured atλ₆₀₀). The dilution was grown for another 1 hour at 37° C. to reach anoptical density of 0.25. At this point, 10 μg/mL of cephalexin was addedto the culture, and a 2-fold serial dilution was made to test a range ofcompound 1 concentrations (0 to 12.5 μM). After the addition ofcompounds, we measured the optical density of cultures. As shown in FIG.9B, cells became filamented and underwent lysis in the presence ofcephalexin. The optical density increases due to cell filamentation(between 1 to 2 hr time points for the sample without compound 1 in FIG.9C) and eventually decreases as cells start lysis. Compared to thispattern in the optical density of the cephalexin-only control, weobserved that cells co-treated with cephalexin and compound 1 elongatedslowly and did not undergo cell lysis, as indicated by the steadyincrease in their optical density (FIG. 9C). This decreased sensitivityto cephalexin in the presence of compound 1 suggests that some latedivision proteins (e.g. amidases) either could not function properly atthe division site, or did not localize to the septum. In summary, thedata presented here collectively indicate that assembly and maturationof the bacterial divisome have been perturbed by compound 1.

Example 8 Inhibition of Cell Division by Compound 1 is Reversible

To test whether the inhibitory effect of compound 1 is reversible, thecompound was washed out of pre-treated cells and their growth anddivision monitored using microscopy. A culture of C. crescentus CB15Ncells was pre-incubated with 6 μM compound 1 for 2.5 hours at 30° C. Asmall aliquot of this culture was applied to an agarose pad (2% w/vagarose in PYE media), and the cells were imaged over time whileincubating them on the microscope stage at 30° C. As shown in FIG. 10,cells were able to grow and resume division as the small moleculediffused out. This relief of inhibition on cell division indicates thatthe inhibitory effect of compound 1 is reversible.

Example 9 Preparation of Compound 1

Compound 1 is prepared by the condensation of 2-hydroxy-1-naphthaldehyde(2) and 3-(2-methyl-1H-benzimidazol-1-yl)propanohydrazide (3). Theintermediate 3 was prepared through the hydrazinolysis of methyl ester5, which in turn was prepared by the reaction of2-methyl-1H-benzimidazole (4) with methyl 3-bromopropionate in thepresence of anhydrous potassium carbonate as a base.

Example 10 Preparation of Compound 6

Compound 6 is prepared similarly to Compound 1 in Example 9 using2-(trifluoromethyl)-1H-benzo [d]imidazole as the starting material.

Example 11 Preparation of Compound 7

Compound 7 is prepared similarly to Compound 1 in Example 9 using2-(trifluoromethyl)-1H-benzo[d]imidazole and 2-methoxy-1-naphthaldehydeas the starting material.

Example 12 Preparation of Compound 8

Compound 8 is prepared similarly to Compound 1 in Example 9 using2-methoxy-1-naphthaldehyde as the starting material.

Example 13 Preparation of Compound 9

Compound 9 is prepared similarly to Compound 1 in Example 9 using2-hydroxy-1-benzylaldehyde as the starting material.

Minimum inhibitory concentration for compounds 1, 6, 7, 8, and 9,determined as in Example 3 using the C. crescentus CB15N strain.

Minimum Inhibitory Compound Concentration, MIC (μM) 1 5 6 7.5 7 >208 >20 9 15

Disclosed herein is a novel class of antimicrobial, specificallyantibacterial compounds, that inhibit cell division in bacteria.Compound 1 and it analogs as described herein are expected to havepotent antibacterial activity, particularly against Gram-negativebacteria. Because of the growing problem of resistance to knownantibiotics such as vancomycin, the development of novel antibiotics isvery important to the treatment of bacterial infections. Compound 1 isbacteriostatic, that is, it inhibits the reproduction of bacterial cellsbut does not kill the microbes. This characteristic reduces theselective pressure on the microbial population for acquisition ofresistant mutations; thus the probability of developing resistance issmaller for the bacteriostatic compound 1.

The use of the terms “a” and “an” and “the” and similar referents(especially in the context of the following claims) are to be construedto cover both the singular and the plural, unless otherwise indicatedherein or clearly contradicted by context. The terms first, second etc.as used herein are not meant to denote any particular ordering, butsimply for convenience to denote a plurality of, for example, layers.The terms “comprising”, “having”, “including”, and “containing” are tobe construed as open-ended terms (i.e., meaning “including, but notlimited to”) unless otherwise noted. Recitation of ranges of values aremerely intended to serve as a shorthand method of referring individuallyto each separate value falling within the range, unless otherwiseindicated herein, and each separate value is incorporated into thespecification as if it were individually recited herein. The endpointsof all ranges are included within the range and independentlycombinable. All methods described herein can be performed in a suitableorder unless otherwise indicated herein or otherwise clearlycontradicted by context. The use of any and all examples, or exemplarylanguage (e.g., “such as”), is intended merely to better illustrate theinvention and does not pose a limitation on the scope of the inventionunless otherwise claimed. No language in the specification should beconstrued as indicating any non-claimed element as essential to thepractice of the invention as used herein.

While the invention has been described with reference to an exemplaryembodiment, it will be understood by those skilled in the art thatvarious changes may be made and equivalents may be substituted forelements thereof without departing from the scope of the invention. Inaddition, many modifications may be made to adapt a particular situationor material to the teachings of the invention without departing from theessential scope thereof. Therefore, it is intended that the inventionnot be limited to the particular embodiment disclosed as the best modecontemplated for carrying out this invention, but that the inventionwill include all embodiments falling within the scope of the appendedclaims. Any combination of the above-described elements in all possiblevariations thereof is encompassed by the invention unless otherwiseindicated herein or otherwise clearly contradicted by context.

1. A pharmaceutical composition, comprising a cell division inhibitorand a pharmaceutically acceptable excipient, wherein the cell divisioninhibitor is of Formula I or a pharmaceutically acceptable salt thereof:G-Q-Y-Z-Ar   (I) wherein G is

wherein each instance of A is independently CH or N provided that thetotal number of N is 0 or 1; R¹ is hydrogen, hydroxy, amino, halogen,cyano, C₁-C₆alkyl, C₁-C₆alkoxy, C₁-C₆haloalkyl, C₁-C₆haloalkoxy, aryl,or (aryl)alkyl; X¹ is N, CR², O, or S; X² is O, S, or NR⁴; R² ishydrogen, C₁-C₆alkyl, C₁-C₆alkoxy, C₁-C₆haloalkyl, C₁-C₆haloalkoxy,aryl, or (aryl)alkyl; each instance of R³ independently is hydroxy,sulfate, nitro, amino, halogen, cyano, C₁-C₄alkyl, C₁-C₄alkoxy,C₃-C₇cycloalkyl, mono- and di-(C₁-C₄alkyl)amino, C₂-C₆alkoxycarbonyl,C₂-C₆alkanoyl, C₁-C₂haloalkyl, C₁-C₂haloalkoxy, phenyl, pyridyl,heterocycloalkyl, alkylcarboxamide, C₂-C₄alkenyl, or C₂-C₄alkynyl; n is0, 1, or 2; m is 0 or 1; Q is a bond or a C₁-C₆ hydrocarbon linkinggroup comprising 0, 1, or 2 heteroatoms chosen from O, S, or NR⁴, andwherein the linking group is substituted by 0, 1, 2, or 3 substituentsindependently chosen from hydroxy, sulfate, nitro, amino, cyano,halogen, C₁-C₄alkyl, C₃-C₇cycloalkyl, C₁-C₄alkoxy, mono- anddi-(C₁-C₄alkyl)amino, C₂-C₆alkoxycarbonyl, C₂-C₆alkanoyl,C₁-C₂haloalkyl, C₁-C₂haloalkoxy, or oxo; R⁴ is hydrogen, C₁-C₆alkyl, orC₁-C₆haloalkyl; Y is —(C═O)NH—N═CH—, —(C═O)NH—, —NH(C═O)—, —(C═O)O—,—O(C═O)— —O(C═O)O—, —NH(C═O)NH—, —NH(C═O)O—, —O(C═O)NH— or —(C═O)—; Z isa bond or a C₁-C₃ hydrocarbon linking group comprising 0, 1, or 2heteroatoms chosen from O, S, or NR⁴, and wherein the linking group issubstituted by 0, 1, 2, or 3 substituents independently chosen fromhydroxy, amino, cyano, halogen, C₁-C₄alkyl, C₃-C₇cycloalkyl,C₁-C₄alkoxy, mono- and di-(C₁-C₄alkyl)amino, C₂-C₆alkoxycarbonyl,C₂-C₆alkanoyl, C₁-C₂haloalkyl, C₁-C₂haloalkoxy, or oxo; Ar is aryl orheteroaryl, substituted with 0, 1, 2, or 3 substituents independentlychosen from hydroxy, sulfate, nitro, amino, cyano, halogen, C₁-C₄alkyl,C₃-C₇cycloalkyl, C₁-C₄alkoxy, mono- and di-(C₁-C₄alkyl)amino,C₂-C₆alkoxycarbonyl, C₂-C₆alkanoyl, C₁-C₂haloalkyl, C₁-C₂haloalkoxy,phenyl, pyridyl, heterocycloalkyl, alkylcarboxamide, C₂-C₄alkenyl, orC₂-C₄alkynyl, and the dashed line in the G structures is a single ordouble bond.
 2. The composition of claim 1, wherein R¹ is hydrogen,fluoro, C₁-C₃alkyl, C₁-C₃alkoxy, C₁-C₃haloalkyl, C₁-C₃haloalkoxy, oraryl.
 3. The composition of claim 2, wherein R¹ is hydrogen, C₁-C₂alkyl,C₁-C₂alkoxy, C₁-C₂haloalkyl, or C₁-C₂haloalkoxy.
 4. The composition ofclaim 3, wherein R¹ is methyl or trifluoromethyl.
 5. The composition ofclaim 4, wherein X¹ is N.
 6. The composition of claim 5, wherein eachinstance of R³ independently is hydroxy, sulfate, nitro, halogen,C₁-C₂alkyl, C₁-C₂alkoxy, C₃-0₅cycloalkyl, mono- anddi-(C₁-C₂alkyl)amino, C₂-C₄alkoxycarbonyl, C₁-C₂haloalkyl, orC₁-C₂haloalkoxy.
 7. The composition of claim 6, wherein Q is a C₁-C₃hydrocarbon linking group substituted by 0, 1, 2, or 3 substituentsindependently chosen from hydroxy, amino, halogen, C₁-C₂alkyl,C₃-C₅cycloalkyl, C₁-C₂₂alkoxy, mono- and di-(C₁-C₂alkyl)amino,C₂-C₄alkoxycarbonyl, C₁-C₂haloalkyl, C₁-C₂haloalkoxy, or oxo.
 8. Thecomposition of claim 7, wherein Y is —(C═O)NH—N═CH—, —(C═O)N—,—NH(C═O)NH—, —NH(C═O)O—, or —O(C═O)NH—.
 9. The composition of claim 8,wherein Z is a bond.
 10. The composition of claim 9, wherein Ar is arylsubstituted with 1 or 2 substituents independently chosen from hydroxy,amino, cyano, halogen, C₁-C₄alkyl, C₃-C₇cycloalkyl, C₁-C₄alkoxy, mono-and di-(C₁-C₄alkyl)amino, C₂-C₆alkoxycarbonyl, C₁-C₂haloalkyl, orC₁-C₂haloalkoxy
 11. The composition of claim 1, wherein the inhibitor isof Formula Ia:

wherein R¹, X¹, R³, n, Q, and Ar are as defined in claim
 1. 12. Thecomposition of claim 11, wherein Ar is naphthalene substituted with ahydroxyl group or a methoxy group, or Ar is phenyl substituted with ahydroxy group.
 13. The composition of claim 12, wherein R¹ is H, CF₃ orCH₃.
 14. The composition of claim 13, wherein Q is C₂alkyl.
 15. Thecomposition of claim 14, wherein the cell division inhibitor is

16-25. (canceled)
 26. The composition of claim 1, wherein G is

wherein each instance of A is independently CH or N provided that thetotal number of N is 0 or 1; R¹ is hydrogen, hydroxy, amino, halogen,cyano, C₁-C₆alkoxy, C₁-C₆haloalkyl, C₁-C₆haloalkoxy, aryl, or(aryl)alkyl; X¹ is N, CR², O, or S; R² is hydrogen, C₁-C₆alkyl,C₁-C₆alkoxy, C₁-C₆haloalkyl, C₁-C₆haloalkoxy, aryl, or (aryl)alkyl; eachinstance of R³ independently is hydroxy, sulfate, nitro, amino, halogen,cyano, C₁-C₄alkyl, C₁-C₄alkoxy, C₃-C₇cycloalkyl, mono- anddi-(C₁-C₄alkyl)amino, C₂-C₆alkoxycarbonyl, C₂-C₆alkanoyl,C₁-C₂haloalkyl, C₁-C₂haloalkoxy, phenyl, pyridyl, heterocycloalkyl,alkylcarboxamide, C₂-C₄alkenyl, or C₂-C₄alkynyl; n is 0, 1, or 2; m is 0or 1; Q is a bond or a C₁-C₆ hydrocarbon linking group comprising 0, 1,or 2 heteroatoms chosen from O, S, or NR⁴, and wherein the linking groupis substituted by 0, 1, 2, or 3 substituents independently chosen fromhydroxy, sulfate, nitro, amino, cyano, halogen, C₁-C₄alkyl,C₃-C₇cycloalkyl, C₁-C₄alkoxy, mono- and di-(C₁-C₄alkyl)amino,C₂-C₆alkoxycarbonyl, C₂-C₆alkanoyl, C₁-C₂haloalkyl, C₁-C₂haloalkoxy, oroxo; R⁴ is hydrogen, C₁-C₆alkyl, or C₁-C₆haloalkyl; Y is —(C═O)NH—N═CH—or —(C═O)NH—; Z is a bond or a C₁-C₃ hydrocarbon linking groupcomprising 0, 1, or 2 heteroatoms chosen from O, S, or NR⁴; Ar is arylsubstituted with 0, 1, 2, or 3 substituents independently chosen fromhydroxy, sulfate, nitro, amino, cyano, halogen, C₁-C₄alkyl,C₃-C₇cycloalkyl, C₁-C₄alkoxy, mono- and di-(C₁-C₄alkyl)amino,C₂-C₆alkoxycarbonyl, C₂-C₆alkanoyl, C₁-C₂haloalkyl, C₁-C₂haloalkoxy,phenyl, pyridyl, heterocycloalkyl, alkylcarboxamide, C₂-C₄alkenyl, orC₂-C₄alkynyl; and the dashed line in the G structures is a single ordouble bond.
 27. The composition of claim 26, wherein G is

wherein each instance of A is independently CH or N provided that thetotal number of N is 0 or 1; R¹ is hydrogen, C₁-C₂alkyl, orC₁-C₂haloalkyl; X¹ is N; each instance of R³ independently is a halogen;n is 0, 1, or 2; m is 0 or 1; Q is a C₁-C₆ hydrocarbon linking group; Yis —(C═O)NH—N═CH—; Z is a bond; Ar is aryl substituted with 0, 1, 2, or3 hydroxy; and the dashed line in the G structures is a double bond. 28.The composition of claim 26, wherein G is

wherein each instance of A is independently CH or N provided that thetotal number of N is 0 or 1; R¹ is hydrogen, C₁-C₂alkyl, orC₁-C₂haloalkyl; X¹ is N; each instance of R³ independently is a halogen;n is 0, 1, or 2; Q is a C₁-C₆ hydrocarbon linking group; Y is—(C═O)NH—N═CH—; Z is a bond; Ar is 1-naphthalenyl substituted with 0, 1,2, or 3 hydroxy; and the dashed line in the G structure is a doublebond.